[gmx-users] image centering

Alan Dodd anoddlad at yahoo.com
Wed Dec 26 11:40:19 CET 2007

Have you tried running trjconv with -centre (selecting SOL, obviously), and then running trjconv -pbc on the result?  I have a vague memory of finding seperating the commands gives a different result, as if the two options were interfering with each other.  What does the output look like when you use the option -centre?  If nothing else, seperating the commands might help you find the source of the problem.

----- Original Message ----
From: Myunggi Yi <myunggi at gmail.com>
To: Discussion list for GROMACS users <gmx-users at gromacs.org>
Sent: Tuesday, December 25, 2007 9:48:29 PM
Subject: [gmx-users] image centering

Dear users,

I have a membrane simulation trajectory,
in which the solvent (water and ions) is separated by lipid bilayer.

I want to center the solvent so that the membrane is separated by two layers at the bottom and top in the unit cell. 

I have tried the followings.

trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -n ../memb.ndx -pbc cluster
trjconv -f ../Eq9/eq9.xtc -o cen2.xtc -s ../Eq9/eq9.gro -n ../memb.ndx -center rect -pbc whole

Both pbc and center didn't work.
Is there any way to center the solvent?

Happy holidays.

Best wishes,

KLB 419
Institute of Molecular Biophysics 
Florida State University
Tallahassee, FL 32306

Office: (850) 645-1334

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